CAS SCIFINDERn

QUICK
REFERENCEGUIDEContents
03 Solution Interface
03-04 References Search
05-06 Substances Search
07 Advanced Search
08 CAS Roles
09-10 Search CAS Sequences
11-12 Reactions Search
13-16 Retrosynthesis Planner
17 Markush and CAS PatentPak®
18 Supplier Search
18 ChemDoodle®
19 Prior Art Analysis
19 Login, Training, and Support

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Solution interface and References search
Main interface
The options below are found on the main interface in CAS SciFindern.

Access CAS Formulus®
and CAS AnalyticalMethodsTM

Click the CAS logo to returnto the main search page

Combinesaved sets

Access alerts, saved items,
history and account settings

Download

Share

Save answers
and create alerts

Search interface
CAS SciFindern features a streamlined search interface.
Execute the search orpress ENTER

Enter the query

Access fielded search, available for
substances and references
Launch thestructure editor

References search result
Performing a References search provides you with access to a full result set inan easy-to-use interface where:– References are default sorted by relevance with customizable sorting options.
– You can focus your answer set further using filters.
– You can save searches, send a link, set up alerts, or add results to a project list.
– You can quickly access full details for any of the references displayed.
View indexed
substances

View indexed
reactions

Save results,
set up alerts
Combine current with saved set
Deselect applied filters

Share answers
Sort answers

Clear all filters

Change how answers
are displayed

Save or addto project

Click title to open reference detail
Load more potentiallyrelevant results

Select Filter by or Exclude, thenselect filter categoriesAccess full-text options

Search any text within
this answer set

Retrieve substance, reaction, or citation data for this reference

Select filters to refine answers

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Reference detail and search operators
Reference detail
Access full details for each reference found in CAS SciFindern.

View forward and backward citations

Publication source information

Get prior art for this patent

Get similar references
PDF displays original patent PDF
PDF+ displays the full text with table of indexed substances
Viewer displays interactive version of annotated full text

Patent family and priority
application information

IPC and indexed
subject matter,
substance indexing,
and formulations

Boolean operators
You can use logical operators to create precise text queries.
Use parentheses to group logical expressions, such as related terms usinng "OR", ex:(flavor or odor) and menthol not cigaretteAND

Requires both terms to be present within the document

OR

Requires either one or both terms to be present (connect synonyms with OR)

NOT

Excludes documents from an answer set containing the word(s) after NOT

Wildcards allow for more comprehensive results in reference, substance, and filter searches.
Internal and right-hand truncation is possible.
*

Replaces 0 to any number of characters

ex: polymorph* | immunoglobulin*conjugate*?

Replaces 0 or 1 character ex: benzonorbornen?

Phrases containing double quotes will be searched as a precise phrase.
Ex: a search for "Programmed cell death protein“ only finds results that exactly match: “Programmed cell
death protein.”
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Substance name and structure search
Substances search
You can search substances by placing one or more substance names or identifiers into the query box.
You can also draw or edit a structure. Below are name search option examples.
Streptomycin
Finds Streptomycin record
57-92-1
Finds Streptomycin record, uses CAS Registry Number® as identifier
Streptomycin sulfate
Finds three records: Streptomycin, Streptomycin sulfate, and Sulfate"Streptomycin sulfate" Streptomycin Finds two records: Streptomycin sulfate and Streptomycin
Sulfoximin*
Finds all names that start with the stem Sulfoximin
WO2019234160
Finds all indexed substances for this patent
Click to draw newstructureEnter chemical name query

Click query structure to edit
Add advanced search fields

Check to perform Markush search

Substances search result

Substances search results are displayed in an intuitive interface where you will see the most relevant
results for your search, including critical property information and high-resolution images.
Select type of structure
match
Change sort criterion
Change amount of details displayed

Click CAS
Registry Number
to open details

Analyze structure
precision

Click on structure toopen flyout window

Start Chemscape Analysis

Search a (sub)structure within
this set of substances

Reference Roles show which new
information was reported about asubstance in the literature

Retrieve data
related to substanceOpen editor withthis structure

Download .sdf or .mol.
Copy Smiles to Clipboard

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Substance detail and structure editor
Substance detail
When you click a CAS Registry Number for one of your Substances search results, substance details
including structure, molecular formula, properties, and further data are displayed.

GHS Hazard pictograms,
Full list in tab at bottomof page

Molecular formula in hill order
Systematic name

Key properties

The chemical identifier list contains SMILES, InChI,
systematic, trivial, and trade names. Names are extracted
from analyzed publications.
Properties and spectra are either listed
or available in linked source publications

CAS Draw editor
You can further define structure and reaction queries using the CAS Draw structure editor.
Import and export structure files

Lasso | Marquee tool
Draw atoms and bonds | Eraser

Enter CAS Registry Number, SMILES,
or InChI to create structure

Learn about keyboard shortcuts
to e.g., easily draw hetero atoms

Hetero atom and H
isotope selection

Pick element symbol from periodic table | Shortcuts
Variable selection | Define own variables (R Groups)
Add attachment point to fragment | Select from templates

Draw bonds. indicate further
options are available

Add positive charge | Add negative charge
Repeating groups | Carbon chain tool
Define variable point of attachment at ring | Reaction role

Draw rings
Resize window

Atom mapping | Lock rings/lock atoms
Bond mapping | Draw reaction arrow

Type element symbol to draw

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Advanced Search
Performing an Advanced Search
You can perform specific References and Substances searches using fields found on the main search
page in CAS SciFindern.
– Operators are processed in this order: OR, AND, NOT– Operators are not available for a search using a single advanced search field– Wildcards are allowed, e.g., peek*– Use up to 50 Advanced Search Fields (49 if also using the main search field)

Change field

General search box

Define operator between search fields
Add more specific fields

Advanced Search examples
Advanced References Search

Advanced Substances Search

Operator to combine search fieldsQuery interpretation:"pollution monitoring" and (polyethyleneor polypropylene)

Query interpretation:
Steel with tensile strength property
information
Click 'Edit Search' to modify
the Advanced Search

Available Advanced Search fields
You can utilize many search fields and categories as part of an Advanced Search query, including:
References Search– Authors– Publication Name
– Organization– Title– Abstract/Keywords– Concept– Substances– Bioactivity Data
– Publication Year– Document Identifier– Patent Identifier– Publisher

Substances Search– Molecular Formula– CAS Registry Number– Chemical Identifier– Document Identifier– Patent Identifier– Experimental Spectra– Bioactivity Data
– Biological– Chemical Properties– Density– Electrical– Lipinski– Magnetic– Mechanical– Optical and Scattering– Structure Related– Thermal

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CAS Roles
CAS Roles overview
Roles are linked to substances, allowing you to find focused publications connecting a substance of interest
to its specific role within the scope of the publication.
– Super roles are broad categories and comprise all related specific roles. Examples are Analytical Study,
Preparation, or Occurrence.
– Specific roles are more precise. They relate to aspects such as the use of the substance in an analytical
study as an analyte (Analyte) or the occurrence of a compound in a plant (Natural Product Occurrence).

Roles in substance results
From a search on substance(s), the roles filter will indicate the types of roles that are connected to thesubstance(s) in the publications.
Example of 'reference roles'
appearing in a substance answer set

Number of substance(s) in theanswer set with that role

Roles in reference results
Roles will appear as a filter in reference result sets whenever you have retrieved hits in the substanceindexing segment of the records, i.e., by retrieving substance names or performing a crossover after
substance-based searches.
Example: I am interested in the subject of (marine) pollution, how can I find publications wherepolypropylene is specifically described as a pollutant?
The search for polypropylene retrieves many references. The substance role window shows all roles that
apply to Polypropylene in this answer set. The Pollutant role indicates there are 3,661 publications that
describe polypropylene as a pollutant. The Search Within function or concepts can be used to restrict
results to marine pollution.

After clicking 'View All‘, more
specific roles can be selected

Every publication in this set of 3,661 references
discusses polypropylene in the context of a pollutant

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Search CAS Sequences
Search options
You can search sequences using three different modalities:– BLAST: Search similar sequences– CDR: Search antibodies and t-cell receptors via CDRs
– Motif: Search using variability symbols

BLAST similarity search
BLAST allows you to search for similar nucleotide and amino acid sequences. Alignment results are shownin an intuitive graphical layout with easy-to-use precision filtering for identity and coverage percentages.
Reference results are linked to the sequence hits.
––––

To perform a BLAST search:
Open the CAS Sequences module from the main CAS SciFindern search page.
Load a sequence from a file or paste a sequence.
Take advantage of supported formats: Sequences containing residues
represented by single-letter codes (e.g., in the FASTA format). Leading
numbers are not allowed.
– Recognize that sequence input may contain a header line (starting with >).
Sequences can be separated by (multiple) headers, thus allowing for batchprocessing.
– Adjust BLAST parameters as desired and start the sequence search.

Sequence Search
options
Upload FASTA sequence from file w/o preceding
numbers or paste into the BLAST pane

Paste sequence
into this window
Include NCBI
sequences

Advanced BLAST
parameters

CAS SciFindern Quick Reference Guide Academic | 9BLAST results analysis
Access results
Sequence search results appear in the Recent Search History and general Search History (Click 'View Results' to view sequence answers.

).

View results
When viewing BLAST sequence similarity results:– Alignments are sorted by Sequence Identity.
– Simplified graphical overview shows alignment quality.
– Mismatches are indicated by red lines.
– Detailed alignments can be viewed in 'Alignment' tab.
– Subject details and patent previews are available in separate tabs.
– Click
to retrieve related references.
– XLSX result download is available.
Get references for all sequences

Query Length
Subject Length

AlignmentDetails

Subject and links to NCBI and substanceinformation in CAS SciFindernMatch

Mismatch

Start of alignment in queryand subject sequences

Reference previews+ Mismatch: Query aa aligned to functional
equivalent subject aa

Alignment Length:49+6=55

Get References
for this sequence

Gap in the query
sequence

Filter results
Filtering dynamically changes your result set.

Expectation Value

Alignment Length

Alignment Length

Number of Matches

Query Length

Subject Length

Alignment Length

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Reactions search
Performing a Reactions search
Reactions queries can be performed using CAS Reaction Numbers, substance names, CAS Registry
Numbers, document identifiers, or a chemical structure.
Select reactions

Click on reaction query to edit

Reactions search results
Reactions search results are grouped into schemes with identical reactants and products or intotransformations. A robust panel of filters, including yield and steps, enables further refinement.
Change grouping to 'By Document‘ or 'By Transformation'

View by structure match

Send to CAS Draw
Click on structure to view
substance information

Yield for displayed reactions

View suppliers

View reaction reference
Filter reaction results

View reaction
details

Access annotatedpatent full-text

Get similar reactions

For single-step, single-stem reactions, you may view similar
reactions based the similarity to of adjacent atoms to the specificreaction center.
•Broad: Retrieve reactions that share a reaction center with theselected reaction.
•Medium: Retrieve reactions that share a reaction center as well asadjacent atoms.
•Narrow: Retrieve reactions with a shared reaction center andextended atoms and bonds.
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Reaction details
Reviewing Reaction details
The details of a reaction provide you with access to information including solvents, catalysts, reagents,conditions, and experimental protocols extracted from the publication and its supplement.
Search for similar reactions

Reaction reference

View all authors

View alternatives

View detailed procedures

View characterization data

Overview of transformations

Further important notes

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Retrosynthesis planner
Launching the tool
There are two primary ways to launch the retrosynthesis tool within CAS SciFindern:
1. Draw or import a structure into the Retrosynthesis window accessed by selecting the Retrosynthesis
option on the main page. The substance can be novel.
2. Choose the Start Retrosynthetic Analysis option found on the substance flyout window.

22
1

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Retrosynthesis planner
Selecting plan options
You can edit plan options to:– Increase the synthetic depth.
– Protect bonds through the entire synthetic route.
– Define bonds to be broken in the first disconnection.
– Change the starting material cost limit.
– Create a predictive plan with more meaningful alternatives, (such as poly- or heterocyclic molecules).
Once you have completed your option selections, choose the Create Retrosynthesis Plan button.
Change the number of
disconnections in the plan

Break bond in first
disconnection

Protect bond inentire plan

Clearselections

Select uncommon or rarerules supported by fewer
literature examples

First bond to be broken

Protected bonds

Change upper cost limit for starting
materials (USD/mol or USD/g)

Generate plan

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Retrosynthesis plan and alternative steps
Open the plan
An Experimental plan is typically available within a few seconds. The calculation of a Predictive
Retrosynthesis Plan can take a bit longer.
Download, Share, and Save your plan
Exclude steps orsubstances

View plan steps

View plan information
Switch predicted
steps on/offShow
experimentalsteps

Edit planoptions
Blue lines mark experimental steps

Green dotted lines
indicate predicted steps

Adjust scoring options

Review and selectalternativedisconnections

Alternative steps
Get an overview of all experimental and predicted disconnections along with the evidence reactions
displayed as a reaction answer set. You can access these evidence reactions from either the (1) link in thesteps overview or (2) alternative reaction scheme.

2Grouped similar reactions

1

Evidence reactions for(predicted) disconnectionof precursor C

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Retrosynthesis scoring options
Scoring options
For plans with predicted steps, you may increase or decrease the score assigned to steps andalternatives by each profile, which determines what is displayed in the plan/alternative steps.
– Each scoring profile may be set to Off (extreme left), Low, Medium, or High (extreme right).
– The default setting for each profile is "Medium" as shown below.
– Moving the slider all the way to the left turns that profile's scoring "Off," and it will not be a factor in step
selection or alternative ranking.

Scoring profiles

CAS SciFindern Quick Reference Guide Academic | 16Markush search and CAS PatentPak
Markush searchMarkush structure searches can be performed using the Search Patent Markush option while in
Substances search mode.

Markush search option
Markushsearch type

Link to a specificpatent reference
Markush location
Assembled Markush
hit structure

Link to CAS PatentPak Viewer

Filter bypatent authority

CAS PatentPak
There are three CAS PatentPak options for viewing a patent PDF:– PDF: Full-text patent PDF only; text-searchable PDF– PDF+: Full-text patent PDF with marked-up Key Substances; text-searchable PDF– Viewer: Patent PDF with linked markups of Key Substances (see below)
Download PDF including list of marked-up substances and annotations
Download PDF
Marks key substancecurated by CAS scientists

Link to related information

Highlighted key
subtance is marked
Link to locationof substance in patent

Key substances identified in thepatent are annotated

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Supplier search and ChemDoodle®
Suppliers search
Using Suppliers search allows you to directly access chemical catalog information based on chemical
structure, names, or other identifiers.

Preferred/non-preferredsupplier tagging

Sort options

Recency ofinformation
Link to detail
Contact information

Catalog details

Order link

ChemDoodle
The ChemDoodle structure editor is available in addition to the standard CAS Draw editor. ChemDoodle isuseful for tablets and mobile devices.
SelectCenter

Flip fragment

Cut | Copy | Paste

Model with CAS Registry Number
Clear | Eraser
Labeling

Templates

Undo | RedoOpen | Save

Draw bonds
Draw rings
Add charges

Zoom

Chain tool
Repeating groups
Variable point of attachment
Lock atoms/chains/rings
Make reaction
Reaction mapping
Break/form bonds

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Prior Art Analysis
Reviewing Prior Art
When viewing a patent Reference Detail page, an option to "Get Prior Art Analysis" is available. Results will
also appear in the search history. This functionality:– Provides an AI-based relevance prediction.
– Is based on a single patent document as the starting point.
– Includes analysis of CAS concepts, indexed substances, IPC codes, and additional full-text.
– Generates a list of relevance-ranked previously known documents, comprising patent andnon-patent literature.

Initiate the analysis fromthe detailed record

View Results from the search history

Login, training, and support
Login details
Log in at scifinder-n.cas.org
Use your existing CAS SciFindern username and password.

Feedback button
Provide direct feedback to CAS from within the CAS SciFindern solution.

Training
Upcoming events and webinars:
www.cas.org/cas-webinars
Recorded events and webinars:
www.cas.org/cas-past-webinars
CAS SciFindern training topics: www.cas.org/support/training/scifinder-nSupport contact
Email help@cas.org to reach a CAS Customer Center representative in North America.
If you are outside of North America, see this website for regional contacts: https://www.cas.org/contact

CAS SciFindern Quick Reference Guide Academic | 19

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